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   <title>Scoring Alignments</title>
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<a name="Scoring_Alignments"></a>Scoring Alignments</h2>
Several different metrics are computed to score each alignment:<br>
<ol>
  <li><span style="text-decoration: underline;">Alignment RMS</span>:
This is the root mean squared distance (in Angstroms) between features
in the aligned conformation and those in the reference pharmacophore.
Lower RMS values correspond to better alignments.</li>
  <li><span style="text-decoration: underline;">Conformation energy</span>:
This is the difference (in kcal/mol) between the computed UFF energies
of the aligned conformation and a baseline conformation of the probe
molecule. The baseline energy is calculated by generating a number of
3D structures of the free probe molecule (not subject to pharmacophore
constraints) and taking the lowest energy. Lower conformation energies
correspond to more stable alignments. Negative conformation energies do
not indicate special stabilization by the pharmacophore, they just
indicate a less-than-perfect value for the baseline energy. :-)</li>
  <li><span style="text-decoration: underline;">Shape score</span>:
this is the Tanimoto similarity between the shape of the aligned
conformation&nbsp; and that of the reference molecule. The shapes are
generated on a Cartesian grid using the van der Waals radii of the
atoms. Higher shape scores indicate better shape matches.<br>
  </li>
</ol>

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